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lindenb · Apr 19, 2024 · 69ca18e · 69ca18e
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diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/WGSCoveragePlotter.java b/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/WGSCoveragePlotter.java
@@ -103,7 +103,7 @@ of this software and associated documentation files (the "Software"), to deal
  * Varani AM, Silva SR, Lopes S, Barbosa JBF, Oliveira D, Correa MA, Moraes AP, Miranda VFO, Prosdocimi F. 2022. The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew. PeerJ 10:e14114 https://doi.org/10.7717/peerj.14114
  * Cho, C.H., Park, S.I., Huang, TY. et al. Genome-wide signatures of adaptation to extreme environments in red algae. Nat Commun 14, 10 (2023). https://doi.org/10.1038/s41467-022-35566-x
  * Rhys T. White, Martina Jelocnik, Natalie Klukowski, Md. Hakimul Haque, Subir Sarker. The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts. Veterinary Microbiology, Volume 280, 2023, 109704, ISSN 0378-1135. https://doi.org/10.1016/j.vetmic.2023.109704.
- * Rhys T. White. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia’s Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris). https://doi.org/10.1099/mgen.0.001101 . Microbial Genomics Vol9 Issue 9
+ * Rhys T. White. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris). https://doi.org/10.1099/mgen.0.001101 . Microbial Genomics Vol9 Issue 9
  * genomic and transcriptomic insight into the evolution and breeding of turfgrass species, poa annua and bouteloua dactyloides. Thesis. Christopher W. Benson. https://etda.libraries.psu.edu/files/final_submissions/29057 **WGSCoveragePlotter**
 
 ## Screenshot

diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/findallcov/FindAllCoverageAtPosition.java b/src/main/java/com/github/lindenb/jvarkit/tools/findallcov/FindAllCoverageAtPosition.java
@@ -99,7 +99,7 @@ of this software and associated documentation files (the "Software"), to deal
 ## Cited in
 
  * Alexandra Bergfort, Tarek Hilal, Benno Kuropka, Ibrahim Avsar Ilik, Gert Weber, Tugce Aktas, Christian Freund, Markus C Wahl, The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling, Nucleic Acids Research, 2022;, gkac087, https://doi.org/10.1093/nar/gkac087
- * Tretter, C., de Andrade Krätzig, N., Pecoraro, M. et al. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 14, 4632 (2023). https://doi.org/10.1038/s41467-023-39570-7
+ * Tretter, C., de Andrade Kratzig, N., Pecoraro, M. et al. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 14, 4632 (2023). https://doi.org/10.1038/s41467-023-39570-7
 
 ## See also
 

diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv.java b/src/main/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv.java
@@ -129,7 +129,7 @@ of this software and associated documentation files (the "Software"), to deal
   * Yang & al. "Sequencing 5-Formyluracil in Genomic DNA at Single-Base Resolution"  (2021) Analytical Chemistry doi: 10.1021/acs.analchem.1c03339
   * Xiao Shu, Chenyang Huang, Tengwei Li, Jie Cao, Jianzhao Liu,.a6A-seq: N6-allyladenosine-based cellular messenger RNA metabolic labelling and sequencing,.Fundamental Research,.2023,.,.ISSN 2667-3258, https://doi.org/10.1016/j.fmre.2023.04.010..(https://www.sciencedirect.com/science/article/pii/S2667325823001267).
   * Xu, Z., Sziraki, A., Lee, J. et al. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01948-9
-  * Braton & al (2023) HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women. Virology. https://doi.org/10.1128/jvi.00705-23
+  * Braton & al (2023) HIVepsilon-seq-scalable characterization of intact persistent proviral HIV reservoirs in women. Virology. https://doi.org/10.1128/jvi.00705-23
 
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diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/vcfpolyx/VCFPolyX.java b/src/main/java/com/github/lindenb/jvarkit/tools/vcfpolyx/VCFPolyX.java
@@ -57,7 +57,7 @@ of this software and associated documentation files (the "Software"), to deal
   * "Multiscale heterogeneity in gastric adenocarcinomaevolution is an obstacle to precision medicine" https://assets.researchsquare.com/files/rs-62554/v1/7883b5d6-a5e6-4d39-8554-e9fef719ac42.pdf
   * Maitena Tellaetxe-Abete, Borja Calvo, Charles Lawrie, Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data, NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab092, https://doi.org/10.1093/nargab/lqab092
   * Pol32, an accessory subunit of DNA polymerase delta, plays an essential role in genome stability and pathogenesis of Candida albicans. Shraddheya Kumar Patel & al. Gut Microbes. https://doi.org/10.1080/19490976.2022.2163840 2023.
-  * Heczko, L., Hlaváč, V., Holý, P. et al. Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases. Cancer Cell Int 23, 295 (2023). https://doi.org/10.1186/s12935-023-03135-x
+  * Heczko, L., Hlavac, V., Holy, P. et al. Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases. Cancer Cell Int 23, 295 (2023). https://doi.org/10.1186/s12935-023-03135-x
 
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